A Novel Splice-Site Mutation in ALS2 Establishes the Diagnosis of Juvenile Amyotrophic Lateral Sclerosis in a Family with Early Onset Anarthria and Generalized Dystonias

Abstract

The diagnosis of childhood neurological disorders remains challenging given the overlapping clinical presentation across subgroups and heterogeneous presentation within subgroups. To determine the underlying genetic cause of a severe neurological disorder in a large consanguineous Pakistani family presenting with severe scoliosis, anarthria and progressive neuromuscular degeneration, we performed genome-wide homozygosity mapping accompanied by whole-exome sequencing in two affected first cousins and their unaffected parents to find the causative mutation. We identified a novel homozygous splice-site mutation (c.3512+1G>A) in the ALS2 gene (NM_020919.3) encoding alsin that segregated with the disease in this family. Homozygous loss-of-function mutations in ALS2 are known to cause juvenile-onset amyotrophic lateral sclerosis (ALS), one of the many neurological conditions having overlapping symptoms with many neurological phenotypes. RT-PCR validation revealed that the mutation resulted in exon-skipping as well as the use of an alternative donor splice, both of which are predicted to cause loss-of-function of the resulting proteins. By examining 216 known neurological disease genes in our exome sequencing data, we also identified 9 other rare nonsynonymous mutations in these genes, some of which lie in highly conserved regions. Sequencing of a single proband might have led to mis-identification of some of these as the causative variant. Our findings established a firm diagnosis of juvenile ALS in this family, thus demonstrating the use of whole exome sequencing combined with linkage analysis in families as a powerful tool for establishing a quick and precise genetic diagnosis of complex neurological phenotypes.

Clinical presentation and natural history of infantile-onset ascending spastic paralysis from three families with an ALS2 founder variant

“…The novel phenotype of JALS/ALS2 associated with generalized dystonia has previously been reported in two unrelated consanguineous families of Bangladeshi and Turkish descent, with homozygous loss of function variants in ALS2 [26]. Shortly thereafter, the same phenotype was described in a large consanguineous Pakistani family with a homozygous splice site variant in ALS2 [27]. Other novel clinical findings in the Bangladeshi family described in the first paper [26] include microcephaly and cerebellar signs, but the authors noted that it is unclear whether these features are caused by the ALS2 pathogenic variant.…”

Genotype-phenotype correlations of amyotrophic lateral sclerosis

“…In the typical adult onset ALS, Alsin gene is rarely mutated [ 30 ]. Recently, a novel splice-site mutation (c.3512 + 1G > A) in Alsin was identified in a consanguineous JALS family with early onset anarthria and generalized dystonia [ 31 ].…”

Genotype-phenotype relationship in hereditary amyotrophic lateral sclerosis

“…Mutations in the Alsin gene cause three distinct disorders: infantile ascending hereditary spastic paraplegia (IAHSP), juvenile primary lateral sclerosis (JPLS), and autosomal recessive juvenile amyotrophic lateral sclerosis (JALS) (Table 1 ) [ 8 , 9 ]. A recent study reported patients with ALS2 with nonsense and frameshift mutations in the Alsin gene who presented with generalized dystonia and cerebellar signs [ 10 ]. Although the phenotype-genotype correlation remains undetermined so far, most of the mutations predict truncated proteins, which could be unstable in structure and lose their function.…”